Abstract
Plant-symbiotic arbuscular mycorrhizal fungi (AMF) are of high global ecological and economic importance, but describing environmental communities of AMF at the species level remains a challenge, despite the need to understand AMF-plant preferences and to apply AMF in sustainable agriculture. Here, the potato-associated AMF species community composition was assessed for three Andean countries along an altitudinal gradient and at different plant stages, by using 454 GS-FLX+ sequencing of a 760 bp LSU rRNA gene PCR amplicon. Two methods were compared: defining OTUs based on a simple sequence similarity threshold, or affiliating reference sequences to species based on a high throughput phylogenetic annotation approach using an evolutionary placement algorithm (EPA). The EPA-based approach was not only more precise, but also fundamental to robustly unveil the AMF species community composition. The principal advantage of this approach was also demonstrated by using artificially constructed datasets based on validated public database sequences. The affiliation of sequence reads to species using phylogenetic annotation revealed a surprisingly conserved AMF core-species community structure in Andean potatoes, regardless of different plant stages and environmental factors. In total, 41 species were detected and in some cases more than 25 species were found colonizing an individual root system. Acaulospora species were identified as dominant colonizers, co-occurring with Cetraspora nodosa and certain Claroideoglomus and Rhizophagus species in most potato root samples.
Highlights
In a world confronted with an increasing human population, one of the main challenges is sustainable food production without negative impacts on valuable natural resources
We wanted to i) validate our new approach by studying whether the interpretation of the arbuscular mycorrhizal fungi (AMF) community structure is principally influenced by the methods used, ii) determine how many and which AMF species live in an individual root system and which AMF co-occur, and iii) analyze whether the AMF species community composition is influenced by altitude and/or plant developmental stage
In each of the three studied countries, Bolivia, Ecuador and Peru, potato roots were sampled at three plant developmental stages, from four potato fields which were located at four different altitude ranges (from 2,658 to 4,075 m above mean sea level)
Summary
In a world confronted with an increasing human population, one of the main challenges is sustainable food production without negative impacts on valuable natural resources. AMF have been found colonizing plants at high altitudes in the Andes, at the Bolivian Altiplano (Urcelay et al 2011) and up to 5,250 m (Schmidt et al 2008), so far there are no studies analyzing the AMF community composition of potato in Andean ecosystems. The SSU-ITS-LSU rRNA gene region used was defined as an extended DNA barcode resolving closely related AMF species (Stockinger et al 2010; Schoch et al 2012) It can be amplified from field samples using AMF specific PCR primers (Krüger et al 2009), which recently were confirmed to have the broadest taxonomic coverage among other PCR primers frequently applied for AMF detection (Kohout et al 2014). We wanted to i) validate our new approach by studying whether the interpretation of the AMF community structure is principally influenced by the methods used, ii) determine how many and which AMF species live in an individual root system and which AMF co-occur, and iii) analyze whether the AMF species community composition is influenced by altitude and/or plant developmental stage
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